It is hypothesized that the genomes of bacterial pathogens are comprised of a core gene pool and a flexible gene pool. The stable core gene pool is inherited clonally and is found in virtually every strain of a species. In contrast, the flexible pool contains genetic elements that are acquired by horizontal gene transfer (HGT). Individual bacterial strains have different constellations of flexible genes that are tailored to their specific life style. Genomic islands (GEIs) are large DNA blocks (10-100kbp) acquired by bacteria via HGT en bloc and constitute important components of the flexible gene pool of bacterial genome. The distinctions between pathogenic and non-pathogenic bacteria in some species have been explained by the acquisition of GEIs by pathogenic strains. Bacteria may also increase their virulence by genomic deletions. In some instances, genomic deletions eliminate inhibitors of virulence factors and allow a full expression of pathogenicity. The Gram-negative facultative bacillus Actinobacillus actinomycetemcomitans (Aa) is a major pathogen in human periodontitis. Individual clones of Aa appear to exhibit differing degrees of pathogenicity and might even employ different virulence mechanisms. Our laboratory has obtained preliminary evidence for the presence of GEIs and smaller genomic islets (of unknown functions) in diverse Aa strains. The insertions of GEIs and slets have lead to truncation and/or inactivation of genes in some Aa strains. Here we test the hypothesis that both GEIs/islets and genomic deletions are common in Aa strains. Furthermore, the gain and loss of genes may change the phenotypes and virulence of Aa. 4 Specific Aims are identified: I) Perform genomic comparison of Aa isolates by DNA microarrays based on the sequenced Aa strain HK1651, II) identify non-HK1651 GEIs/islets in Aa by PCR genomic mapping followed by cloning and sequencing, III) Examine the expression of Aa GEIs/islets and their impact to the gene expression profiles of Aa, IV) Assess the stability of Aa genome over time by arrays. The research plan is expected to (i) generate a thorough catalogue of GEIs/islets and large DNA deletions in the genomes of diverse Aa strains, (ii) obtain evidence for the expression (and possibly the functions) of GEIs/islets, (iii) examine the gene expression profiles of Aa with or without the presence of GEIs/islets, (iv) obtain evidence for the genomic instability of Aa over short periods of time (years), (v) identify new candidate virulence factors of Aa and (vi) elucidate the genetic basis of the phenotype and virulence variations of Aa. The results are likely to further the progress in the field of periodontal disease pathogenesis.